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1SZ6
Biol. Unit 1
Info
Asym.Unit (98 KB)
Biol.Unit 1 (179 KB)
(using Jmol or JSmol)
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(1)
Title
:
MISTLETOE LECTIN I FROM VISCUM ALBUM. CRYSTAL STRUCTURE AT 2.05 A RESOLUTION
Authors
:
A. G. Gabdoulkhakov, N. E. Guhlistova, A. V. Lyashenko, R. Krauspenhaa S. Stoeva, W. Voelter, S. V. Nikonov, C. Betzel, A. M. Mikhailov
Date
:
04 Apr 04 (Deposition) - 05 Oct 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Ribosome-Inactivating Protein Type Ii, Hydrolase Inhibitor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. G. Gabdoulkhakov, N. E. Guhlistova, A. V. Lyashenko, R. Krauspenhaar, S. Stoeva, W. Voelter, S. V. Nikonov, C. Betzel, A. M. Mikhailov
Crystal Structure Of Viscum Album Mistletoe Lectin I In Native State At 2. 05 A Resolution, Comparison Of Structure Active Site Conformation In Ricin And In Viscumin
To Be Published
[
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Hetero Components
(4, 46)
Info
All Hetero Components
1a: AZIDE ION (AZIa)
1b: AZIDE ION (AZIb)
1c: AZIDE ION (AZIc)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
3k: GLYCEROL (GOLk)
3l: GLYCEROL (GOLl)
3m: GLYCEROL (GOLm)
3n: GLYCEROL (GOLn)
3o: GLYCEROL (GOLo)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AZI
6
Ligand/Ion
AZIDE ION
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
GOL
30
Ligand/Ion
GLYCEROL
4
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
SO4
2
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(24, 24)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ILE B:11 , VAL B:12 , ASN B:44 , ASN B:136 , HOH B:3109 , HOH B:3132 , HOH B:3159 , HOH B:3294
BINDING SITE FOR RESIDUE NAG B 5001
02
AC2
SOFTWARE
TRP B:94 , ASN B:96 , TYR B:126 , LEU B:228 , HOH B:3166 , HOH B:3318 , GOL B:4013
BINDING SITE FOR RESIDUE NAG B 5002
03
AC3
SOFTWARE
LYS A:90 , ASP A:91 , ASN A:112 , HOH A:3213 , HOH A:3224 , HOH A:3271
BINDING SITE FOR RESIDUE NAG A 5003
04
AC4
SOFTWARE
ASP B:27 , PHE B:29 , ASN B:61 , HOH B:3134 , HOH B:3136 , HOH B:3296
BINDING SITE FOR RESIDUE NAG B 5004
05
AC5
SOFTWARE
GLU A:119 , HIS A:124 , ARG A:125 , ASP A:126
BINDING SITE FOR RESIDUE SO4 A 4001
06
AC6
SOFTWARE
GLN B:30 , ASP B:31 , HOH B:3135
BINDING SITE FOR RESIDUE AZI B 4003
07
AC7
SOFTWARE
ASP A:211 , ASN A:232 , HOH A:3242 , ILE B:93 , LEU B:133 , ALA B:134
BINDING SITE FOR RESIDUE AZI A 4004
08
AC8
SOFTWARE
VAL B:218 , PHE B:219 , HOH B:3144 , HOH B:3145 , HOH B:3146
BINDING SITE FOR RESIDUE AZI B 4005
09
AC9
SOFTWARE
GLN A:205 , HIS A:208 , ASN A:216
BINDING SITE FOR RESIDUE CL A 4021
10
BC1
SOFTWARE
ASP B:235 , GLN B:238 , TYR B:249 , ASN B:256 , HOH B:3152
BINDING SITE FOR RESIDUE GOL B 4006
11
BC2
SOFTWARE
TYR A:1 , ARG A:3 , LEU A:55 , HOH A:3055
BINDING SITE FOR RESIDUE GOL A 4007
12
BC3
SOFTWARE
SER A:32 , ARG A:41 , GLN A:42
BINDING SITE FOR RESIDUE GOL A 4008
13
BC4
SOFTWARE
GLY A:63 , ASP A:64 , SER A:65 , ARG A:143 , HOH A:3038 , HOH A:3039 , GOL A:4019
BINDING SITE FOR RESIDUE GOL A 4009
14
BC5
SOFTWARE
ALA A:92 , PRO A:93 , GLY A:95 , ALA A:96 , GLU A:97 , THR A:98
BINDING SITE FOR RESIDUE GOL A 4010
15
BC6
SOFTWARE
ARG A:175 , ASP A:189 , LEU A:222 , PRO A:223 , TYR B:146
BINDING SITE FOR RESIDUE GOL A 4011
16
BC7
SOFTWARE
ASP B:23 , VAL B:24 , ARG B:25 , ASP B:26 , GLN B:36 , TRP B:38 , LYS B:41 , ASN B:47 , HOH B:3101 , HOH B:3238
BINDING SITE FOR RESIDUE GOL B 4012
17
BC8
SOFTWARE
LEU B:228 , HOH B:3228 , NAG B:5002
BINDING SITE FOR RESIDUE GOL B 4013
18
BC9
SOFTWARE
ARG A:154 , TYR B:68 , ALA B:72 , GLN B:122 , THR B:123 , HOH B:3097 , HOH B:3173 , HOH B:3178
BINDING SITE FOR RESIDUE GOL B 4014
19
CC1
SOFTWARE
PRO A:129 , GLN A:134 , PHE B:79 , ALA B:84 , VAL B:85 , HOH B:3079 , HOH B:3143 , HOH B:3174
BINDING SITE FOR RESIDUE GOL B 4015
20
CC2
SOFTWARE
PRO A:171 , ARG A:175 , GLN A:178 , HOH A:3009 , TYR B:146 , ASP B:150
BINDING SITE FOR RESIDUE GOL A 4016
21
CC3
SOFTWARE
ARG B:59 , ASN B:82 , HOH B:3316
BINDING SITE FOR RESIDUE GOL B 4017
22
CC4
SOFTWARE
ARG A:234 , ASP A:235 , HOH A:3022 , ARG B:141 , LEU B:176 , HOH B:3021 , HOH B:3052 , HOH B:3085
BINDING SITE FOR RESIDUE GOL B 4018
23
CC5
SOFTWARE
GLN A:84 , ARG A:143 , HOH A:3201 , GOL A:4009
BINDING SITE FOR RESIDUE GOL A 4019
24
CC6
SOFTWARE
SER A:148 , THR A:149 , ARG A:150 , HOH A:3266 , ASN B:105
BINDING SITE FOR RESIDUE GOL A 4020
[
close Site info
]
SAPs(SNPs)/Variants
(19, 38)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_ML1_VISAL_001 (A15D, chain A, )
02: VAR_ML1_VISAL_013 (N18S, chain B, )
03: VAR_ML1_VISAL_014 (G56N, chain B, )
04: VAR_ML1_VISAL_002 (N112T, chain A, )
05: VAR_ML1_VISAL_003 (P116T, chain A, )
06: VAR_ML1_VISAL_004 (T140S, chain A, )
07: VAR_ML1_VISAL_005 (F144Y, chain A, )
08: VAR_ML1_VISAL_006 (T151A, chain A, )
09: VAR_ML1_VISAL_015 (G157Q, chain B, )
10: VAR_ML1_VISAL_007 (Y179D, chain A, )
11: VAR_ML1_VISAL_008 (A184E, chain A, )
12: VAR_ML1_VISAL_009 (V190M, chain A, )
13: VAR_ML1_VISAL_016 (N194V, chain B, )
14: VAR_ML1_VISAL_010 (I218F, chain A, )
15: VAR_ML1_VISAL_017 (G223Y, chain B, )
16: VAR_ML1_VISAL_018 (N230S, chain B, )
17: VAR_ML1_VISAL_019 (N230T, chain B, )
18: VAR_ML1_VISAL_011 (T231S, chain A, )
19: VAR_ML1_VISAL_012 (D235S, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_ML1_VISAL_001
*
E
48
D
ML1_VISAL
---
---
A
A
15
D
02
UniProt
VAR_ML1_VISAL_013
*
N
319
S
ML1_VISAL
---
---
B
N
18
S
03
UniProt
VAR_ML1_VISAL_014
*
G
357
N
ML1_VISAL
---
---
B
G
56
N
04
UniProt
VAR_ML1_VISAL_002
*
N
145
T
ML1_VISAL
---
---
A
N
112
T
05
UniProt
VAR_ML1_VISAL_003
*
P
149
T
ML1_VISAL
---
---
A
P
116
T
06
UniProt
VAR_ML1_VISAL_004
*
T
173
S
ML1_VISAL
---
---
A
T
140
S
07
UniProt
VAR_ML1_VISAL_005
*
F
177
Y
ML1_VISAL
---
---
A
F
144
Y
08
UniProt
VAR_ML1_VISAL_006
*
T
184
A
ML1_VISAL
---
---
A
T
151
A
09
UniProt
VAR_ML1_VISAL_015
*
G
458
Q
ML1_VISAL
---
---
B
G
157
Q
10
UniProt
VAR_ML1_VISAL_007
*
Y
212
D
ML1_VISAL
---
---
A
Y
179
D
11
UniProt
VAR_ML1_VISAL_008
*
A
217
E
ML1_VISAL
---
---
A
A
184
E
12
UniProt
VAR_ML1_VISAL_009
*
V
223
M
ML1_VISAL
---
---
A
V
190
M
13
UniProt
VAR_ML1_VISAL_016
*
C
495
V
ML1_VISAL
---
---
B
N
194
V
14
UniProt
VAR_ML1_VISAL_010
*
I
251
F
ML1_VISAL
---
---
A
I
218
F
15
UniProt
VAR_ML1_VISAL_017
*
G
524
Y
ML1_VISAL
---
---
B
G
223
Y
16
UniProt
VAR_ML1_VISAL_018
*
N
531
S
ML1_VISAL
---
---
B
N
230
S
17
UniProt
VAR_ML1_VISAL_019
*
N
531
T
ML1_VISAL
---
---
B
N
230
T
18
UniProt
VAR_ML1_VISAL_011
*
T
264
S
ML1_VISAL
---
---
A
T
231
S
19
UniProt
VAR_ML1_VISAL_012
*
D
268
S
ML1_VISAL
---
---
A
D
235
S
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: RICIN_B_LECTIN ()
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RICIN_B_LECTIN
PS50231
Lectin domain of ricin B chain profile.
ML1_VISAL
309-436
440-563
4
B:8-135
B:139-262
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 3)
Info
All SCOP Domains
1a: SCOP_d1sz6b1 (B:1-137)
1b: SCOP_d1sz6b2 (B:138-263)
2a: SCOP_d1sz6a_ (A:)
View:
Select:
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Classes
(
)
(
)
Folds
(
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
beta-Trefoil
(385)
Superfamily
:
Ricin B-like lectins
(91)
Family
:
Ricin B-like
(65)
Protein domain
:
Plant cytotoxin B-chain (lectin)
(21)
European mistletoe (Viscum album) [TaxId: 3972]
(12)
1a
d1sz6b1
B:1-137
1b
d1sz6b2
B:138-263
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ribosome inactivating proteins (RIP)
(180)
Superfamily
:
Ribosome inactivating proteins (RIP)
(180)
Family
:
Plant cytotoxins
(166)
Protein domain
:
Mistletoe lectin I A-chain
(11)
European mistletoe (Viscum album) [TaxId: 3972]
(11)
2a
d1sz6a_
A:
[
close SCOP info
]
CATH Domains
(3, 4)
Info
all CATH domains
1a: CATH_1sz6A01 (A:1-167)
2a: CATH_1sz6A02 (A:168-248)
3a: CATH_1sz6B01 (B:2-139)
3b: CATH_1sz6B02 (B:140-263)
View:
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Architectures
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Ricin (A subunit); domain 1
(112)
Homologous Superfamily
:
Ricin (A subunit), domain 1
(112)
European mistletoe (Viscum album)
(14)
1a
1sz6A01
A:1-167
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Ricin (A Subunit), domain 2
(112)
Homologous Superfamily
:
Ricin (A Subunit), domain 2
(112)
European mistletoe (Viscum album)
(14)
2a
1sz6A02
A:168-248
Class
:
Mainly Beta
(13760)
Architecture
:
Trefoil
(289)
Topology
:
Trefoil (Acidic Fibroblast Growth Factor, subunit A)
(289)
Homologous Superfamily
:
[code=2.80.10.50, no name defined]
(289)
European mistletoe (Viscum album)
(14)
3a
1sz6B01
B:2-139
3b
1sz6B02
B:140-263
[
close CATH info
]
Pfam Domains
(2, 3)
Info
all PFAM domains
1a: PFAM_Ricin_B_lectin_1sz6B01 (B:139-259)
1b: PFAM_Ricin_B_lectin_1sz6B02 (B:139-259)
2a: PFAM_RIP_1sz6A01 (A:6-209)
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Clans
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Families
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(
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Organisms
(
)
(
)
Clan
:
Trefoil
(131)
Family
:
Ricin_B_lectin
(25)
Viscum album (European mistletoe)
(9)
1a
Ricin_B_lectin-1sz6B01
B:139-259
1b
Ricin_B_lectin-1sz6B02
B:139-259
Clan
:
no clan defined [family: RIP]
(62)
Family
:
RIP
(62)
Viscum album (European mistletoe)
(9)
2a
RIP-1sz6A01
A:6-209
[
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]
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